title: IST536 MM15 cells, exponential, biol rep 2

city: Lisbon

first: Isabel

last: Sá-Correia

address: Avenida Rovisco Pais, 1

department: Department of Bioengineering

country: Portugal

institute: Instituto Superior Técnico

data_processing:
Reads containing adapter sequences, containing poly-N, or low quality reads were removed from raw data using Trimmomatic
Paired-end clean reads were aligned using HISAT2 v2.2.0 (--phred33 --dta)
read count was performed using featureCounts from the Subread package v2.0.4
Differential expression analysis was performed using the DESeq2 R package v1.42.0
Assembly: GCA_963855905 (not public yet)
Supplementary files format and content: tab-delimited text files include the output from DESeq2

organism: Rhodotorula toruloides

source_name: yeast

growth_protocol: Cells grown in minimal medium (2% glucose, 0.69% YNB)

extract_protocol:
RNA extraction was performed by using a modified hot phenol method, described in Amin-ul Mannan et., Analytical Biochemistry, (2009), and then purified using the commercial kit RNA Clean & Concentrator-5 (Zymo Research)
RNA libraries preparations were carried out by  Novogene Bioinformatics Technology for Illumina sequencing

value: yeast

value: Evolved strain


title: 3V007, scRNAseq + CITE-seq

status: Public on May 29 2024

type: SRA

city: New York

first: Patrick

last: Wilson

state: NY

address: 413 E. 69th Street

department: gale and Ira Drukier Institute for Children's Health

country: USA

institute: Weill Cornell Medicine

description: 10x Genomics

library_source: transcriptomic

data_processing:
Cellranger Single-Cell Software Suite (version 6.1.2) was used to perform sample de-multiplexing, barcode processing, and single-cell 5’ and V(D)J counting, and Cellranger mkfastq was used to de-multiplex raw base call (BCL) files into sample-specific fastq files. Subsequently, reads were aligned to the GRCh38 human genome. Cellranger counts and Cellranger vdj package within the Cellranger pipeline were used to identify gene expression and assemble V(D)J pairs of antibodies.
Assembly: GRCh38-2020-A
Supplementary files format and content: compressed tar.gz file, has barcodes.tsv, genes.tsv, matrix.mtx 3 files, which are outputs from CellRanger pipeline

molecule: total RNA

organism: Homo sapiens

source_name: Blood Cells

extract_protocol:
Chromium next GEM single cell 5' HT v2 protocol
The libraries were constructed based on the 10X Genomics protocols for  5’ gene expression, BCR V(D)J and cell surface protein mapping library construction.
Libraries were sequenced using an Illumina NextSeq1000 at the Weill Cornell Medicine.

tag: tissue

value: Blood Cells


title: hUCB_healthy donor4

type: RNA

city: Palma

first: Josep

last: Muncunill Farreny

address: Carretera de Valldemossa, 79. Hospital Universitario Son Espases

country: Spain

institute: IdISBa

hyb_protocol: Samples were hybridized with GeneChip Human Clariom D Arrays (Affymetrix, Thermo Fisher Scientific) and scanned at the IdISBa Genomic Core Facility.

scan_protocol: Array scanning was performed by using the GeneChip Scanner 3000 7G according to the manufacturer's instruction (Affymetrix, Thermo Fisher Scientific).

data_processing: Preprocessing was performed in R/Bioconductor using the oligo package. Raw CEL files were summarized and normalized through RMA (Robust Multichip Average) and quantile normalization (oligo::rma). Quality control analyses were performed with arrayQualityMetrics package. Probes were annotated with packages pd.clariom.s.human, clariomshumantranscriptcluster.db and annotation file from Affymetrix (Clariom S Array, human Transcript Cluster Annotations, CSV, Release 36).

label: biotin

source_name: umbilical cord blood cells from heathy donor

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the GeneChip WT Plus Reagent Kit (Affymetrix, Thermo Fisher Scientific) and then fragmented and biotin-labeled with the WT Terminal Labeling Kit (Affymetrix, Thermo Fisher Scientific).

growth_protocol: Cells were grown in flasks coated with rat tail collagen type I high concentration and cultured in EGM-2 Endothelial Cell Growth Medium-2 BulletKit (CC-3162).

extract_protocol: Total RNA was extracted using QIAzol Lysis Reagent from miRNeasy Mini Kit following the manufacturer's protocol.

treatment_protocol: During pregnancy, fetus was exposed to OSA conditions caused by OSA-affected mother.

value: human umbilical cord blood cells

tag: developmental stage

value: Newborn

tag: disease state

value: Healthy


title: IST536 cells, exponential, biol rep 2

tag: cell type

tag: genotype

value: WT


title: IST536 MM15 cells, exponential, biol rep 1


title: hUCB_healthy donor3


title: hUCB_patient3

source_name: umbilical cord blood cells from SAHS patient

value: SAHS affected


title: hUCB_patient2


title: IST536 cells, exponential, biol rep 1


title: hUCB_healthy donor1


title: hUCB_healthy donor2


title: G4IMA Patient 11

city: Boston

first: Eric

last: Grewal

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

hyb_protocol: RNA was hybridized using the NanoString nCounter® CodeSet Hybridization kit according to manufacturer instructions, and then were loaded onto a NanoString nCounter® Prep Station.

scan_protocol: Samples were subjected to RNA-sequencing on the NanoString nCounter® Digital Analyzer using default settings according to manufacturer instructions for the nCounter Human (GPL27981) or Mouse (GPL30135) Innate Immunity Panel V2.

data_processing: After RNA sequencing, each raw sample file (.RCC format) was uploaded to the automated RNA-sequencing data processing and analysis software, Rosalind (Rosalind Bio). These files underwent automatic read mapping, normalization, and quality control.

label: NanoString labels

source_name: Grade 4 IDH-mutant astrocytoma

label_protocol:
Total RNA was measured using the Aligent Bioanalyzer 2100 and NanoDrop 2000 prior to hybridization.
Labeling according to standard Nanostring protocol.

extract_protocol: Formalin-fixed, paraffin-embedded tissue blocks were cut, deparaffinized, and digested, and RNA was isolated uisng the Qiagen Rneasy Mini Kit (74134).

value: Grade 4 IDH-mutant astrocytoma

tag: idh status

value: Mutant


title: hUCB_patient1


title: G4IMA Patient 09


title: G4IMA Patient 10


title: G4IMA Patient 08


title: hUCB_patient5


title: G4IMA Patient 12


title: G4IMA Patient 07


title: G4IMA Patient 06


title: Cp_Glc_Log_Rep1

city: Baltimore

first: Jeffrey

middle: G.

last: Gardner

state: MD

address: 1000 Hilltop Circle

department: Department of Biological Sciences

institute: University of Maryland - Baltimore County

description:
Cp_Glc_TPM.csv
Necromass_DEG.xlsx

data_processing:
The raw FASTQ files were quality checked, aligned to existing genomes, and analyzed for differential expression using the Galaxy platform. Unless otherwise noted below, default parameters were in all analysis tools used except in cases where strandedness was specified (all RNAseq data were unstranded). Briefly, RNAseq data were concatenated using the concatenate data sets: tail-to-head (cat) tool. Transcript quality was tested using FastQC, which indicated read trimming was unnecessary for any of the files. Transcripts were next aligned to their respective reference genomes using the HISAT2 tool and quantified using the htseq-count tool. Reference genome files for C. japonicus Ueda107 (ASM1922v1) and C. pinensis DSM2588 (ASM2400v1) were obtained from ENSEMBLE, while that for S. marcescens PIC3611 was retrieved from NCBI Refseq (ASM2260299v1). Due to the differences in reference genome sources, the S. marcescens files required a parameter change in the htseq-count ‘feature type’ from ‘gene’ to ‘exon’. Differential gene expression using DESeq2 compared necromass exponential growth to necromass stationary phase for all three species and glucose for Cp and Sm.
Assembly: C. japonicus Ueda107 (ASM1922v1); C. pinensis DSM2588 (ASM2400v1); S. marcescens PIC3611 (ASM2260299v1)
Supplementary files format and content: TPM for biolgical repliates for a given substrate and bacterial species; DEG with p-values for pair-wise comparisons

organism: Chitinophaga pinensis

source_name: Bacterial cell

extract_protocol:
As per the protocol described in PMID: 22949721
Ribosomal RNA Depletion; RNA Fragmentation and Random Priming; Fist and Second Strand cDNA synthesis; End Repair with 5' phosphorylation and dA-Tailing; Adapter ligation with PCR enrichment; Sequencing

tag: strain

value: Bacterial cell

tag: group

value: Glc

tag: growth phase

value: Log


title: G4IMA Patient 02


title: G4IMA Patient 05


title: G4IMA Patient 03


title: GBM Patient 12

source_name: Glioblastoma

value: Glioblastoma

value: Wildtype


title: GBM Patient 09


title: GBM Patient 10


title: GBM Patient 11


title: GBM Patient 08


title: Human lung tissue cells  IAV infected

city: Hannover

first: Frank

last: Pessler

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Experimental Infection Research

country: Germany

institute: TWINCORE Centre for Experimental and Clinical Infection Reearch

description: Single cell transcriptome from total 2220 human human lung tissue . Cell were infected with IAV.

library_source: transcriptomic single cell

data_processing:
Cell Ranger 1.3 (http://10xgenomics.com) was used to process Chromium  single  cell  3’  RNA-seq  output
cellranger count aligned to the pre-built human reference genome (hg19, GRCh38)
Raw counts were normalized by the global-scaling normalization method “LogNormalize”.
Principal component analysis score was used to determine the ‘dimensionality’ of all cells.
Scatter plots were obtained using the UMAP method. Cell clusters were identified as different cell populations based on the expression of recently published canonical markers
Assembly: human reference genome (hg19, GRCh38) and Influenza A virus
Supplementary files format and content: filtered_feature_bc_matrix, tsv and mtx files
Supplementary files format and content: Seurat object

molecule: polyA RNA

source_name: Lung

growth_protocol: Bronchial lung tissue explanted from patients with terminal COPD for clinical reasons was obtained from the Institute of Pathology, Hannover Medical School. The tissue was further dissected into small pieces with an average size of approx. 27 mm3 (3x3x3 mm) and an average weight of approx. 30 mg. These pieces (HLTEs) were cultured in RPMI medium without any supplement. Tissue pieces were cultured overnight in a humidified tissue culture incubator at 37°C, 5% CO2; this step was termed overnight washing.

extract_protocol:
After 24 hpi, tissues were collected and processed to prepare a single-cell suspension for flow cytometry and cell sorting. Briefly, lung tissues were chopped in digestion buffer (1 mg/ml collagenase D (Roche, 10269638001), 2.0 U/ml Dispase II (Roche, 04942078001) and 0.1 mg/ml DNase I (DNase I, D4527) in Hepes-buffer) with surgical scissors and homogenized with an Ultra-Turrax® dispersing tool (T10, IKA-Werke GmbH, Staufen, Germany) for 40-60 sec. The homogenate was incubated for 30 minutes at 37°C with mild agitation and then passed through a 30G syringe. The resulting single-cell suspension was filtered through a 40 µm nylon cell strainer and erythrocytes were lysed using ACK (Ammonium-Chloride-Potassium) lysing buffer. Cells were counted using an automated cell counter (Scepter, Millipore, PHCC00000).
Single-cell 3’ RNA-Seq libraries were prepared using Chromium Single Cell V3 Reagent Kit and Controller (10x Genomics) as described in the user guide. In brief, cells (n=4500) for a targeted recovery of 3500 along with gel beads, master mix and partitioning oil were loaded in designated wells on a chromium chip. The chip was placed in a Chromium Controller and run for Gel Bead-in-Emulsion (GEMs) preparation. After completion of the run, GEMs were run in PCR tubes for RT incubation in a thermal cycler. Post GEM-RT incubation, cDNA was cleaned up and amplified. cDNA was washed and quality was evaluated. Gene expression libraries were constructed and then libraries were assessed for quality (TapeStation 4200, Agilent). Libraries were sequenced by NextSeq550 using the NextSeq 500 High Output Kit v2.5 (1x75 cycles 400M cluster).

treatment_protocol: AfterAfter 12-16 h of washing, tissues were infected with the respective pathogen.

value: Lung

value: Primary

value: COPD

tag: treatment

value: IAV infected


title: GBM Patient 04


title: GBM Patient 06


title: GBM Patient 02


title: GBM Patient 03


title: Human lung tissue cells uninfected control

description: Single cell transcriptome from total 2964 human lung tissue untreated. Cell were uninfected and untreated.

value: uninfected


title: GBM Patient 05


title: D09-25-2

city: charlottesville

first: Shefali

last: Banerjee

state: Virginia

address: 622 Noush court

institute: University of Virginia

data_processing:
STAR v. 2.7.10a
basecalling illumina RTA 2.11.3.0
Sequence reads were trimmed for adpator sequences/low quality sequence using cutadapt v.1.15
Trimmed sequence reads were mapped to hg38 reference genome and counted reads using STAR 2.7.9a with parameter --outFilterType BySJout --outfilterMultimapNmax 20 --alignIntronMax 1000000 --alignMateGapMax 1000000 --alignSJoverhangmin 8 --alignSJDBoverhangmin 1 --quantMode GeneCounts
DESeq2 1.42.0
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Supplementary files format and content: tab-delimited text file include normalized counts for each sample

source_name: HeLa

extract_protocol:
Total RNA was isolated using Direct-zol RNA miniprep kit from Zymoresearch.
RNA libraries were prepared using NEBNext polyA mRNA Magnetic Isolation Module and NEB Ultra II RNA library preparation kit for illumina following manufacturer's protocol

tag: cell line

value: HeLa

value: cervical cancer immortalized cell line

value: 25nM of siRNA siD09 targeting DDX39A


title: D09-25-3


title: GBM Patient 01


title: G4IMA Patient 04


title: D06-25-2

value: 25nM of siRNA siD06 targeting DDX39A


title: NSC-25-3

value: 25nM of control siRNA 5nM transfected


title: D06-25-3


title: NSC-25-2


title: D09-25-1


title: GBM Patient 07


title: G4IMA Patient 01

value: Grade 4 IDH-mutant astrocytoma


title: NSC-25-1


title: D13-5-3

value: 5nM of siRNA siD13 targeting DDX39B


title: hUCB_patient4

value: human umbilical cord blood cells

value: Newborn

value: SAHS affected


title: D13-5-1


title: NSC-5-1

value: 5nM of control siRNA 5nM transfected


title: NSC-5-3


title: D11-5-1

value: 5nM of siRNA siD11 targeting DDX39B


title: BamRNAi h3k36me3

first: BiNGS

last: Core

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

library_source: genomic

data_processing:
Reads were evaluated for their quality using FastQC v0.11.8
Reads were trimmed for adaptor sequences using Trim Galore! v0.6.6
Reads were aligned to the dm6 reference genome version for drosophila melanogaster using Bowtie2 v2.2.8 with parameters -q -I 50 -X 700 --very-sensitive-local --local --no-mixed --no-unal --no-discordant
Binary alignment maps (BAM) files were generated with samtools v1.9
MACS2 v2.1.0 was used to call significant peaks for samples BamRNAi Stwl, WT Stwl and WT BEAF. IgG was used as control to call peaks. Peaks within ENCODE blacklisted regions and repetitive sequences larger than 100 bases were removed
BigWig files were generated from BAM files using deepTools v3.2.1 bamCoverage function with parameters– normalize using RPKM–bin size 10
Assembly: dm6
Supplementary files format and content: bigWig, bed (for BamRNAi Stwl, WT Stwl and WT BEAF)
Library strategy: CUT&RUN

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: Ovary tissue

growth_protocol: Ovaries dissected in 1x PBS.

extract_protocol:
PBS was removed and the samples were permeabilized in 1mL of Permeabilization Solution (PBST+1% Triton-X) rotating in RT for 1 hour. Samples were then incubated overnight at 4°C in primary antibody dilutions in freshly prepared BBT+ buffer (PBST + 1% BSA + 0.5 mM Spermidine + 2 mM EDTA + 1 large Roche complete EDTA-free tablets). Primary antibody was replaced with BBT+ buffer and quickly washed twice. Samples were then incubated in ~700 ng/ml of pAG-MNase in BBT+ buffer rotating for 4 hours at 25°C. Samples were then quickly washed twice in wash+ buffer (20 mM HEPES pH7.5 + 150 mM NaCl + 0.1% BSA + 0.5 mM Spermidine + 1 large Roche complete EDTA-free tablets in water). Samples were resuspended in 150 μl Wash+C (wash+ + 100 mM CaCl2) and incubated for 45 minutes on nutator at 4°C. The cleavage reaction was terminated by addition of 150 μl StopR (NaCl final 200 mM + EDTA final 20 mM + 100μg/mL RNaseA) and incubating the sample at 37˚C for 30 minutes. Samples were then centrifuged at 16,000 x g for 5 minutes and 300 μl of the supernatant was collected for DNA discovery. To the supernatant, 2 μL 10% SDS and 2.5 μL of 20 mg /mL Proteinase K was added and incubated at 50°C for 2 hours. Half of this was kept as a backup and half was used in bead cleanup. 20 μL AmpureXP bead slurry and 280 μL MXP buffer (20% PEG8000 + 2.5 M NaCl + 10 mM MgCl2 in water) was added to the sample and mixed thoroughly followed by 15 minutes incubation at RT. The beads were separated by magnet and supernatant was discarded. The beads were carefully washed with 80% ethanol for 30 seconds, while on the magnetic stand and air dried for 2 minutes. The beads were then resuspended in 10 μL DNase free water.
The samples from CUT&RUN assay were used for library preparation using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7645, E7103) and adaptor ligated DNA were prepared without size selection.
The samples from CUT&RUN assay were used for library preparation using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (E7645, E7103) and adaptor ligated DNA were prepared without size selection.

value: Undifferentiated stages

value: Ovary tissue

value: BamRNAi

tag: chip antibody

value: H3K36me3 ab (abcam AB9050)


title: StwlRNAi h3k4me1

value: Differentiated stages

value: StwlRNAi

value: H3K4me1 ab epicypher (13-004)


title: StwlRNAi h3k36me3


title: NSC-5-2

value: HeLa

value: cervical cancer immortalized cell line


title: StwlRNAi h3k27ac

value: H3K27ac ab (abcam AB4729)


title: StwlRNAi h3k9me3

value: H3K9me3 ab (Active motif 39062)


title: BamRNAi h3k4me3

value: H3k4me3 ab (abcam AB8580)


title: StwlRNAi h3k4me3


title: BamRNAi h3k9me3


title: StwlRNAi h3k27me3

value: H3K27me3 ab (abcam AB6002)


title: BamRNAi h3k27me3


title: BamRNAi h3k27ac


title: BamRNAi h3k4me1


title: WT h3k27me3

value: WT


title: D11-5-2


title: WT h3k36me3


title: WT h3k4me1


title: IgG

value: IgG Jackson immunoResearch Laboratories 006-000-003


title: BEAF stwl GKD

value: stwl GKD

value: BEAF DSHB AB_1553420


title: WT h3k4me3


title: WT h3k27ac


title: BEAF WT


title: Stwl stwl GKD

value: Stwl ab made by the Jagannathan Lab


title: Stwl WT

value: Ovary tissue


title: Stwl bam GKD

value: Undifferentiated stages

value: bam GKD


title: BVDV Transient Infection on Gestation Day 175:  Postnatal Day 0 PBMC DNA 2183

city: Fort Collins

first: Thomas

last: Hansen

state: CO

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

data_processing:
Quality of reads were checked with fastqc 0.11.9, reads were trimmed with trimgalore 0.6.4_dev
Reads were mapped to the bosTau9 genome using bismark 0.22.3
Obtained bam files were analyzed with methylKit 1.24.0
Assembly: bosTau9
Supplementary files format and content: bedGraph files generated from bismark for each sample
Supplementary files format and content: comma-delimited files for differentially methylated cytosines and regions

organism: Bos taurus

source_name: PBMC

extract_protocol:
DNA was extracted from WBCs processed from whole blood using Qiagen DNeasy Blood and Tissue Kit (Qiagen, Hilden, Germany).
DNA samples were digested with 30 units of MspI, fragments purified with DNA Clean & Concentrator-5  and ligated to adapters with replacement of cytosine with 50-methyl-cytosine according to Illumina’s guidelines. Fragments greater than 50 base pairs were recovered and bisulfite treated using the EZ DNA Methylation-Lightning Kit . Samples were subjected to PCR with Illumina indices. Size and concentrations of purified products were confirmed with the Agilent 2200 TapeStation prior to sequencing on an Illumina platform

value: PBMC

value: White Blood Cells

value: BVDV Transient Infection


title: BVDV Transient Infection on Gestation Day 175:  Postnatal Day 0 PBMC DNA 2186


title: Control Gestation Day 175: Postnatal Day 0 PMBC DNA 2149

description: CpGi: Islands

value: control


title: BVDV Transient Infection on Gestation Day 175:  Postnatal Day 0 PBMC DNA 2106


title: Control Gestation Day 175: Postnatal Day 0 PMBC DNA 2156

description: CpGi: Islands


title: Control Gestation Day 175: Postnatal Day 0 PMBC DNA 2147

description: CPG sites hypomethylated


title: BVDV Transient Infection on Gestation Day 175:  Postnatal Day 0 PBMC DNA 2103

description: CpGp: Promoters


title: Control Gestation Day 175: Postnatal Day 0 PMBC DNA 2163

description: CpGp: Promoters


title: Distended vein, canine 3, ST

city: Cartersville

first: Marina

last: Michaud

state: GA

address: 28 Cass Station Dr NW

department: School of Medicine

institute: Emory University

description:
C3-ST2, 10x Genomics, Visium
GVV11_C3-ST2

data_processing:
*library strategy: Spatial transcriptomics
For spatial transcriptomics samples, demultiplexing, barcoded processing, gene counting, aggregation, and spatial alignment were performed using the 10x SpaceRanger software (v.2.0.0).
Assembly: Dog10K_Boxer_Tasha_1.0
Supplementary files format and content: Tab-separated value files for barcodes and genes with matrix files
Supplementary files format and content: Spatial alignment output files for spatial transcriptomics

organism: Canis lupus familiaris

source_name: Cephalic vein

extract_protocol:
For spatial transcriptomic analysis, Frozen samples embedded in O.C.T. (TissueTek Sakura) were cryosectioned (10 mm sections) at −20 ºC and transferred onto pre-chilled Visium Tissue Optimization Slides (10x Genomics, 3000394) and Visium Spatial Gene Expression Slides (10x Genomics, 2000233). H&E staining was performed according to the Visium Spatial Gene Expression User Guide (10x Genomics, CG000239 rev. F). For the Visium spatial transcriptomics gene expression assay, tissue was permeabilized for the optimal time (9 minutes).
For spatial transcriptomics,  following tissue permeablization, reverse transcription, second strand synthesis and denaturation, cDNA amplification and QC, and gene expression library construction according to 10x Genomics user guide (CG000239 rev. F) was performed.The gene expression libraries were quantified using a Qubit fluorometer (Thermo Fisher Scientific) and checked for quality using DNA HS bioanalyzer chips (Agilent).

treatment_protocol: Bilateral upper limb cephalic vein harvest was performed on 25 kg male (n=3) or female (n=1) mongrel dogs (Marshall Bioresources). General anesthesia was established and maintained with an initial sodium pentothal injection and subsequent 1% isofluorane inhalation after orotracheal intubation. Vein harvest was performed in conventional fashion. The cephalic vein was identified and exposed along the anterior surface from the wrist to the upper forearm. The distal portion of the vein was then ligated and transected. The end of the transected vein was cannulated with a metal cannula and secured with a silk suture. The vein was then sequentially distended by injecting a saline solution (0.9% sodium chloride, papaverine hydrochloride 60 mg, and 43 mg of bivalirudin) while occluding the outflow. Intervening tributaries were identified and ligated with silk sutures. A total length of 15 cm of vein was harvested. Total vein distension and harvest time was approximately 30 minutes. The cephalic vein following distention, along with a separate segment of the undistended cephalic vein, which served as the experimental control, were excised. Samples were collected and immediately snap-frozen in cryovials using liquid nitrogen for single-nuclei analysis or embedded in OCT blocks and flash-frozen in an isopentane and liquid nitrogen bath for spatial transcriptomics analysis. Systemic bivalirudin was then infused before the creation of the anastomoses. Bilateral end-to-side anastomoses were created on the vein with 7-0 Prolene sutures. The intervening segment of the carotid artery was then ligated, creating preferential flow through the graft. After hemostasis was achieved, the wounds were closed in three layers with 3-0 vicryl sutures. The patency of the graft was confirmed through direct palpation and ultrasound imaging. At 24 hours, harvest was performed with the dog under general anesthesia. Vein graft samples were then collected and processed as previously described for cryopreservation and OCT embedding.

value: Cephalic vein

value: Endothelial cells, smooth muscle cells, fibroblasts, myeloid cells

tag: Sex

value: Male

value: Distension


title: Control Gestation Day 175: Postnatal Day 0 PMBC DNA 2132

description: CpG sites hypermethylated


title: WT h3k9me3

value: Differentiated stages

value: H3K9me3 ab (Active motif 39062)


title: Control vein, canine 3, ST

description:
C3-ST1, 10x Genomics, Visium
GVV10_C3-ST1

value: Control


title: Control vein, canine 4, ST

description:
C4-ST1, 10x Genomics, Visium
GVV13_C4-ST1

value: Female


title: Distended vein, canine 4, ST

description:
C4-ST2, 10x Genomics, Visium
GVV14_C4-ST2


title: Control vein, canine 2, ST

description:
C2-ST1, 10x Genomics, Visium
GVV8_C2-ST1


title: Distended vein, canine 2, ST

description:
C2-ST2, 10x Genomics, Visium
GVV5_C2-ST2


title: Grafted vein, canine 1, ST

description:
C1-ST3, 10x Genomics, Visium
GVV9a_C1-ST3

value: Grafted


title: Distended vein, canine 2, snRNA-seq

description:
C2-SN2, 1\0x Genomics, Chromium Nuclei
GVN7_C2-SN2

data_processing:
For snRNA-seq samples, demultiplexing, barcoded processing, gene counting, and aggregation were performed using the 10x CellRanger software (v.7.0.0).
Assembly: Dog10K_Boxer_Tasha_1.0
Supplementary files format and content: Tab-separated value files for barcodes and genes with matrix files

molecule: nuclear RNA

extract_protocol:
For single-nuclei analysis, we used the sample prep user guide (10x Genomics, CG000505, Rev A) for the Chromium Nuclei Isolation Kit with RNase Inhibitor (10x Genomics, 1000494) to isolate nuclei from flash-frozen tissues. The various buffers (lysis, debris removal, wash, and resuspension buffers) were prepared using kit components according to user guide instructions (10x Genomics, CG000505, Rev A). Briefly, ~50 mg of tissue, cut into smaller pieces to enable better lysis of cells, was added to pre-chilled sample dissociation tubes and dissociated by adding lysis buffer followed by multiple strokes with the pestle against the dissociation tubes. Following incubation on ice for 10 minutes, the dissociated tissue was added to the nuclei isolation column, placed in a pre-chilled collection tube, and spun at 16,000 g for 20 sec at 4oC. The flowthrough was collected, vortexed to resuspend the nuclei, and spun at 500g, 3 min, 4oC. The pellet was then resuspended in debris removal buffer, pipet mixed, and spun at 700 g, 10 min, 4oC. After discarding the supernatant, the pellet was washed with wash and resuspension buffer by spinning at 500 g, 5min, 4oC. For counting, the nuclei were stained with acridine orange/propidium iodide stain (Logos Biosystems) and counted using a LUNA-FX7 cell counter (Logos Biosystems). The nuclei pellet was resuspended in wash and resuspension buffer to get the desired nuclei concentration (700-1200 nuclei/ml).
For snRNA-seq, gene expression libraries were prepared immediately from the isolated nuclei with the Chromium Next GEM Single Cell 3’ v3.1 reagent kits (10x Genomics, 1000268). Briefly, GEMs were prepared using the 10x Genomics controller followed by RT-PCR and cDNA amplification. The cDNA was then used to prepare snRNA-seq libraries according to the user guide (10x Genomics, CG000315 rev. B). The quality of the cDNA and final library preps was assessed using DNA HS bioanalyzer kits (Agilent), and concentration was estimated using a Qubit fluorometer (Thermo Fisher Scientific).


title: Control vein, canine 2, snRNA-seq

description:
C2-SN1, 10x Genomics, Chromium Nuclei
GVN4_C2-SN1


title: Distended vein, canine 1, snRNA-seq

description:
C1-SN2, 10x Genomics, Chromium Nuclei
GVN3_C1-SN2


title: Grafted vein, canine 1, snRNA-seq

description:
C1-SN3, 10x Genomics, Chromium Nuclei
GVN2_C1-SN3


title: Control vein, canine 1, snRNA-seq

description:
C1-SN1, 10x Genomics, Chromium Nuclei
GVN1_C1-SN1


title: PB CD34+ HSPCs, SF3B1 mutant, , SMARTseq

city: Pavia

first: Martina

last: Sarchi

address: Via Ferrata 9

department: Dept. of Molecular Medicine

country: Italy

institute: University of Pavia

description: SMARTSeq v4 Ultra Low Input RNA Kit

data_processing:
For gene expression analysis, reads were pseudoaligned using kallisto.
Differential gene expression was determined using the DESeq2 package.
For splicing analysis, RSEM v1.2.4 was used to map all RNA-seq reads to this transcriptome annotation.
Remaining unaligned reads were then mapped a database of all possible junctions between annotated 5' and 3' splice sites of the transcriptome annotation, as well as to the genome sequence, with TopHat v2.0.8b, and the resulting aligned reads were merged with the RSEM output
The expression levels of isoforms annotated in MISO v2.0’s annotation were estimated with MISO v2.0.
To identify events that were differentially spliced, we defined the metric deltaPSI (ΔPSI) as the isoform ratio (absolute percentage of mRNA) in SF3B1-mutant samples - isoform ratio in SF3B1-WT cells, and computed a significance statistic using Wagenmakers’s Bayesian framework for single-sample comparisons or the Mann-Whitney U test for group comparisons. An event was classified as differentially spliced if it exhibited an absolute change of ΔPSI ≥ 10% and Bayes factor ≥ 5 or p < 0.05.
Assembly: For splicing analysis, transcriptome annotation for the hg19/GRCh37 human genome assembly was created by merging gene annotations from Ensembl v71.1, the UCSC knownGene track, and MISO v2.0 isoform annotations.
Assembly: For gene expession analysis, hg38 reference genome was used.
Supplementary files format and content: comma-separated values file including splicing analysis for CB CD34+ HSPCs including dPSI and PSI values.
Supplementary files format and content: comma-separated values file including splicing analysis for PB CD34+ HSPCs including dPSI and PSI values.
Supplementary files format and content: comma-separated values file including splicing analysis for PB CD34+ HSPCs (SMARTSeq v4 Ultra Low Input RNA Kit) including dPSI and PSI values.
Supplementary files format and content: comma-separated values file including normalised counts for CD34+ HSPCs.
Supplementary files format and content: comma-separated values file including paiwise comparison between SF3B1 mutant and AAVS1 control CD34+ HSPCs.
Supplementary files format and content: comma-separated values file including splicing analysis for K562 cells including dPSI and PSI values.
Supplementary files format and content: comma-separated values file including normalised counts for K562 cells.
Supplementary files format and content: comma-separated values file including paiwise comparison between SF3B1 mutant and wild-type K562 cells.

source_name: Hematopoietic

growth_protocol:
HSPCs were cultured in StemSpan SFEM II (StemCell Technologies), 100 U/mL penicillin/streptomycin (Fisher), 100 ng/ml SCF, 100 ng/ml FLT3, 100 ng/ml TPO, 100 ng/ml IL-6 (all Peprotech), 35 nM UM171 (Apexbio Technology) and 0.75 μM SR1 (Cellagen Technology). Cell density was maintained between 4 x 10^5 and 1 x10^6 per ml.
SF3B1-mutant (K700E) and wild-type control K562 cells (25) were grown in Iscove’s modified Dulbecco’s media (IMDM) with 10% FBS and 100 U/mL penicillin/streptomycin (Fisher), and cultures were maintained at <1.5 x 10^6 cells/ml.

extract_protocol:
Cells were resuspended in Trizol (ThermoFisher, cat. #15596026), and RNA extracted per manufacturer protocol.
RNA sequencing was performed at Omega Bioservices with TruSeq Stranded mRNA kit with polyA selection. PB BFP+CD34+ gene edited HSPCs were additionally sequenced with SMARTSeq v4 Ultra Low Input RNA Kit.

treatment_protocol: HSPCs were CRISPR-edited using the Lonza 4D Nucleofection system and the Human Primary Cell Nucleofection Kit (Lonza). RNP complexes were generated by combining Cas9 protein and sgRNA (Synthego) at 1:2.5 molar ratio in P3 Primary Cell Nucleofector Solution with Supplement 1 (Lonza). CD34+ HSPCs were electroporated using Lonza 4D (DZ-100 program) and returned to HSPC media containing AAV particles comprising < 20% culture volume, as recommended. HSPCs were washed 16-24 hours later and plated in HSPC media for 48 hours.

value: Hematopoietic

value: CD34+ HSPCs from mobilized peripheral blood


title: K562 MUT replicate 1

description: TruSeq Stranded mRNA kit with polyA selection


title: BVDV Transient Infection on Gestation Day 175:  Postnatal Day 0 PBMC DNA 2169


title: PB CD34+ HSPCs, SF3B1 mutant


title: PB CD34+ HSPCs, AAVS1 control, SMARTseq

description: SMARTSeq v4 Ultra Low Input RNA Kit


title: CB CD34+ HSPCs,  AAVS1 control

value: CD34+ HSPCs from cord blood


title: MUT2_rep1

city: CHENNAI

first: SOWMYA

last: PARAMESWARAN

address: 41 COLLEGE ROAD

country: India

institute: VISION RESEARCH FOUNDATION

data_processing:
Based on quality report of fastq files sequence reads were trimmed where necessary. Low-quality sequence reads are excluded from the analysis. The adapter trimming was performed using Trimmomatic (v-0.36).Contamination removal was performed using Bowtie2 (2.2.4).
The paired-end reads are aligned to the reference human genome (hg19). Alignment was performed using HISAT2 (2.1.0).
The raw read counts were estimated using FeatureCount (1.5.2).
DESeq was used to calculate the differentially expressed transcripts.
Assembly: Human genome (hg19)
Supplementary files format and content: tab-delimited text file format of normalised count for each sample

source_name: iPSC

growth_protocol: RB-iPSCs were derived from orbital adipose mesenchymal stem cells of RB patients. The RB-iPSCs were cultured on geltrex coated tissue culture plates and maintained in E8 essential medium at 37C in 5%CO2.

extract_protocol:
Total RNA was isolated from the RB-iPSC derived retinal organoids using TRIZOL reagent (sigma).
RNA sequencing library was prepared following manufacturer's protocol. Illumina-compatible sequencing libraries were quantified by Qubit fluorometer and fragment size distribution was analyzed. The libraries were paired-end sequenced on Illumina Sequencer

treatment_protocol: The iPSCs were dissociated as small clusters and cultured in DMEM-F12 supplemented with 1% N2 supplement and heparin (2mg/ml) for one week to form cell aggregates. The cell aggregates were plated onto  coated 24-well plate and differentiated for 2-3 weeks in the differentiation medium with N2 supplement prior to shifting them to DMEM-F12 containing 2% B27 supplement. During the differentiation period structures resembling anterior neuro-epithelium (rosette like); primitive eye field structures (dense cellular central portions with lighter periphery with horse-shoe shaped structures) were observed. The horse-shoe shaped structures were excised and cultured in suspension in medium containing 2% B27 for further 2 weeks. The medium was replaced to retinal maturation medium containing Taurine (50μM) and Shh (100ng/ml) to promote maturation of neural retina.Retinal organoids were harvested at 120 days.

value: iPSC

value: retinal differentiation


title: MUT1_rep2


title: MUT2_rep2


title: MUT1_rep1


title: WT2_rep2


title: Control vein, canine 1, ST

description:
C1-ST1, 10x Genomics, Visium
GVV1_C1-ST1


title: WT2_rep1


title: WT1_rep2


title: WT1_rep1


title: MB231_TWEAK_p52_rep2

city: Singapore

first: Yinghui

last: Li

state: Singapore

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

data_processing:
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using Bowtie2
Peaks were called using MACS2 with subtraction of input signal (the input used is GSM7286594).
bigwig files were generated using deepTools
Assembly: hg38
Supplementary files format and content: bigwig, bed

source_name: Breast

growth_protocol: Cell lines were seeded in DMEM + 10% FBS. After 24h, cells were starved in optimem for 8h then treated with 10ng/ml TWEAK for 48h. TWEAK was replenished after 24h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Diagenode Bioruptor. DNA was sheared to 200-500bp.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol

value: Breast

value: Breast Cancer

value: TWEAK


title: z5929_Normal_input

data_processing:
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using Bowtie2
Peaks were called using MACS2 with subtraction of input signal
bigwig files were generated using deepTools
Assembly: hg38
Supplementary files format and content: bigwig

extract_protocol:
Tissue samples were fixed with 1% formaldehyde for 10 minutes. After quenching, tissue samples were homogenized and lysed before the chromatin was sonicated using a Diagenode Bioruptor. DNA was sheared to 200-500bp.
ChIP-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol

value: Normal Breast


title: MB231_TWEAK_p52_rep1


title: z6122_Normal_input


title: z6122_Tumour_input


title: z5929_Tumour_input


title: z8370_Normal_input


title: K562 MUT replicate 2


title: Mixed stage total nuclei, replicate 3

city: Stanford

first: Callista

last: Yee

state: California

address: 327 Campus Drive, Shen lab, Bass Biology 329

institute: Stanford University/HHMI

data_processing:
All dataprocessing was conducted using ENCODE consortium's atac-seq pipeline. Briefly,  cutadapt 1.9.1 was used to trim read adapters from fastqs
Fastqs were aligned to worm genome using Bowtie2 version 2.2.6, SAMtools 1.7, SAMstats (version 0.2.1)
Post-alignment filtering was performed using SAMtools (1.7) MarkDuplicates (Picard - latest version 1.126) bedtools 2.26 to remove unmapped reads and duplicates
Peak calling was performed using MACSv2 (2.1.0) (P-value thresholds (-p [P-VAL-THLD] in MACS2 parameter) 0.01 is used.)
IDR 2.0.4 (IDR_THRESH=0.05) was performed on MACS2 called peaks
Assembly: ce11
Supplementary files format and content: .narrowPeaks represent ATAC-seq peaks from sorted nuclei

organism: Caenorhabditis elegans

source_name: All Cells

growth_protocol: Worms were grown at 20C on standard NGM agar with OP50 bacteria.

extract_protocol:
Worms were washed 3X with M9 and dounced in ChIP Buffer A for 10 strokes usng a steel dounce. Nuclei suspension was spun down for 1 minute at 100g, and passed through a 5mL cell filter tube. Nuclei morphology was assessed by DAPI, and subjected to flow cytometry for sorting.
Tn5 tagmented DNA was amplified as previously described (Buenrostro et al., 2015), using ATAC optimized primers. Amplification was monitored using qPCR, and additional cycles of library amplication was performed as needed. DNA was analyzed on a Bioanalyzer and submitted for Illumina HiSeq.

value: All Cells

value: Mixed stage


title: z8850_Tumour_input


title: PB CD34+ HSPCs, AAVS1 control


title: CB CD34+ HSPCs, SF3B1 mutant


title: Mixed stage total nuclei, replicate 2


title: Mixed stage total nuclei, replicate 1


title: z8370_Tumour_input


title: z2086_Normal_input


title: Mixed stage neuronal nuclei, replicate 3

source_name: Neurons

value: Neurons


title: z5929_Normal_K27


title: z6122_Normal_K27


title: z8850_Tumour_K27


title: z5929_Tumour_K27


title: Mixed stage neuronal nuclei, replicate 2


title: z8850_Normal_input


title: z8850_Normal_K27


title: Mixed stage neuronal nuclei, replicate 1


title: z6122_Tumour_K27


title: z2963_Normal_input


title: 8pool-AS, scRNAseq + CITE-seq

description: 10x Genomics

value: Blood Cells


title: z2963_Tumour_input


title: z2963_Normal_K27


title: in vitro, tRFs released from synthesized tRNA, replicate 3

city: Barcelona

first: Jiarui

address: Campus UAB  Cerdanyola del Valles (Bellaterra)

institute: Universitat Autònoma de Barcelona

description:
tRNAAspGTC.csv
tRNAGlnCTG.csv
tRNALysCTT.csv
tRNALysTTT.csv
tRNAMetCAT.csv
tRNALysTTT.fa
tRNALysCTT.fa
tRNAMetCAT.fa
tRNAAspGTC.fa
tRNAGlnCTG.fa

library_source: other

data_processing:
Reads was trimmed with Cutadapt (v1.9.1)
The pair-end reads were merged by BBmerge
Use linux command to merge all three replicates
Use linux command to change the .fastq file from sequence to .fasta file which can be aligned
Use MAFFT online service to align .fasta file to reference sequence, which include the five tRNAs sequences together
Assembly: > tRNA LysTTT LysCTT MetCAT AspGTC GlnCTG
Assembly: GGGCGGATAGCTCAGTCGGTAGAGCATCAGACTTTTAATCTGAGGGTCCAGGGTTCAAGTCCCTGTTCGCCCGGGGCGGCTAGCTCAGTCGGTAGAGCATGGGACTCTTAATCTCAGGGTCGTGGGTTCGAGCCCCACGTTGCCCGCCAGGGCTCTTAGTGCAGCTGGCAGCGCGTCAGTTTCATAATCTGAAGGTCGTGAGTTCGATCCTCACACGGCCCACCGGGTCATCAGTATAGTGGTGAGTATCCCCGCCTGTCACGCGGGAGACTGGGGTTCGATTCCCTGAGGACCCGCCAGGGTCCATGGTGTAATGGTGAGCACTCTGGACTCTGAATCCAGCGATCCGAGTTCGAGTCTCGGTGGACCCTCCA
Supplementary files format and content: alignment file (.fa) processed by Jalview (v2.11) for each tRNA

molecule: other

extract_protocol:
Synthetic tRNAs were incubated with RNase 2 and the digestion products from five selected tRNAs were purified separately by equal volume of acid-phenol: chloroform and pelleted by ethanol precipitation. The pellets were later dissolved in DEPC-treated water and mixed altogether.
The mixed samples were firstly treated with CIP to remove the phosphates on both terminals and then we added T4 PNK, supplemented with ATP, to ensure that all tRFs started with a 5’monophosphate and ended with 3’ hydroxyl. Following purification by the acid-phenol procedure (chloroform extraction and ethanol precipitation), 100 ng of the mixture were ligated with adaptors, reverse transcription and amplification was performed according to the manufacturer’s protocol of NEBNext® Multiplex Small RNA Library Prep Set for Illumina®.

value: RNase 2 degradation in vitro


title: z2963_Tumour_K27


title: z8370_Tumour_K27


title: in vitro, tRFs released from synthesized tRNA, replicate 2


title: z8370_Normal_K27


title: z2086_Normal_K27


title: z5929_Normal_ATAC

data_processing:
Adaptors were removed using Trimmomatic
Reads were mapped to hg38 using Bowtie2
Mitochondrial reads were removed using Bamtools
Duplicate reads were removed using Picard
Peaks were called using MACS2
Assembly: hg38
Supplementary files format and content: bigwig files
Supplementary files format and content: Bed files containing called peaks

extract_protocol:
Tissue samples were homogenised and nuclei was isolated through iodixanol density gradient centrifugation. Nuclei were then transposed with digitonin and Tn5 transposase
Transposed DNA was amplified through PCR with Nextera DNA CD Indexes


title: z6122_Normal_ATAC


title: z8850_Normal_ATAC


title: z5929_Tumour_ATAC


title: in vitro, tRFs released from synthesized tRNA, replicate 1


title: z2086_Tumour_K27


title: z2086_Tumour_input


title: z6122_Tumour_ATAC


title: z8850_Tumour_ATAC


title: z2963_Tumour_ATAC


title: CAMA1_TWEAK_RNA-seq_rep3

data_processing:
Trimmomatic was used to remove adaptor sequences.
Reads were mapped to hg38 using STAR
featureCounts was used to extract raw counts
Differential analysis was performed with DESeq2
Assembly: hg38
Supplementary files format and content: bed file containing raw counts

extract_protocol:
RNA was extracted using Trizol and treated with Dnase.
RNA-seq libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB; E7645) according to the manufacturer’s protocol through the polyA mRNA workflow


title: CAMA1_TWEAK_RNA-seq_rep2


title: z2086_Tumour_ATAC


title: z8370_Normal_ATAC


title: z8370_Tumour_ATAC


title: CAMA1_TWEAK_RNA-seq_rep1


title: z2086_Normal_ATAC


title: CAMA1_UT_RNA-seq_rep3

value: Untreated


title: z2963_Normal_ATAC


title: CAMA1_UT_RNA-seq_rep2


title: MCF7_TWEAK_RNA-seq_rep3


title: MCF7_UT_RNA-seq_rep3


title: MCF7_UT_RNA-seq_rep1


title: MCF7_TWEAK_RNA-seq_rep1


title: Hs578T_TWEAK_RNA-seq_rep1


title: Hs578T_UT_RNA-seq_rep3


title: CAMA1_UT_RNA-seq_rep1


title: Hs578T_UT_RNA-seq_rep2


title: MCF7_UT_RNA-seq_rep2


title: Hs578T_TWEAK_RNA-seq_rep3


title: Hs578T_TWEAK_RNA-seq_rep2


title: MCF7_TWEAK_RNA-seq_rep2


title: MB231_UT_RNA-seq_rep3


title: MB231_TWEAK_RNA-seq_rep2


title: MB231_UT_RNA-seq_rep1


title: MB231_TWEAK_RNA-seq_rep3


title: CAMA1_input


title: MB231_UT_RNA-seq_rep2


title: Hs578T_UT_RNA-seq_rep1


title: MB231_TWEAK_RNA-seq_rep1


title: CAMA1_TWEAK1_K27_rep2


title: CAMA1_TWEAK1_K27_rep1


title: CAMA1_UT_K27_rep2


title: CAMA1_UT_K27_rep1


title: MCF7_input


title: MCF7_TWEAK1_K27_rep1


title: MCF7_UT_K27_rep2


title: MCF7_TWEAK1_K27_rep2


title: Hs578T_input


title: Hs578T_TWEAK_K27_rep3


title: MCF7_UT_K27_rep1


title: Hs578T_TWEAK_K27_rep2


title: Hs578T_UT_K27_rep3


title: Cell_BJF_Trajectory_B_PDL_52_Replicate_1

type: genomic

city: San Diego

first: Morgan

middle: E.

last: Levine

state: CA

address: 5510 Morehouse Dr

department: Institute of Sciences San Diego

institute: Altos Labs

hyb_protocol: EZ-96 DNA Methylation-Lightning™ MagPrep (Zymo)

scan_protocol: iScan Illuminias settings

data_processing:
SESAME
Beta Values

label: Cy3 and Cy5

label_protocol: Standart Illumina

growth_protocol: Cells were routinely cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS (REF: 10437-028), 1x Gibco MEM Non-Essential Amino Acids (REF: 11140-050), and 1x GlutaMax (REF: 35050079)

extract_protocol: DNeasy Blood and Tissue Kit (Qiagen 69504)

value: Male

value: Fibroblast


title: Human FL Tfh exon-level [PGD_929_HTA]

city: Rennes

first: Stephane

last: Rodriguez

state: France

address: 2, Av Pr. Leon Bernard

country: France

institute: INSERM

description:
PGD_929_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis

hyb_protocol: 4.7 μg of cDNAs were hybridized for 16 hours at 45oC on GeneChip® Human Transcriptome Array 2.0 (Affymetrix). The chips were washed and stained in the GeneChip® Fluidics Station 450 (Affymetrix)

scan_protocol: Chip were scanned with the GeneChip® Scanner 3000 7G (Affymetrix) at a resolution of 0.7 µm.

data_processing: CEL files were further processed with Affymetrix Expression Console software version 1.3.1 using Robust Multi-array Average (RMA) algorithms with default settings at the gene and exon levels.

source_name: Follicular Lymphoma donor

label_protocol: Biotinylated double strand cDNA targets were prepared, starting from 25 ng of total RNA for all samples except PGD-926 for which we used 15 ng, with the NuGEN Ovation Pico WTA System V2 Kit (Cat # 3302) followed by the NuGEN Encore Biotin Module Kit (Cat # 4200) according to manufacturer recommendations.

extract_protocol:
Lymphoid cells were recovered by perfusion of FL lymph node (LN) biopsies or non-malignant tonsils, enriched using Ficoll gradient
First, CD19+/CD14+/CD8+/CD16+ cell populations were targeted by their dedicated mouse anti-human monoclonal antibody, Second : an incubation with goat anti-mouse magnetic beads allowed CD4+ T enrichement. Third, subsets of interest were sorted according to their known phenotype using a FACSAria flow cytometer
RNA was isolated from 0,5 to 10M sorted cells with the RNeasy AllPrep Micro Kit (Qiagen), according to the manufacturer’s instructions.

value: Lymph node


title: Human FL Memory CD4 exon-level [PGD_928_HTA]

description:
PGD_928_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Cell_BJF_Trajectory_B_PDL_45_Replicate_1


title: Hs578T_TWEAK_K27_rep1


title: Hs578T_UT_K27_rep2


title: Hs578T_UT_K27_rep1


title: Human FL Memory CD4 exon-level [PGD_932_HTA]

description:
PGD_932_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human FL Tfr exon-level [PGD_931_HTA]

description:
PGD_931_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Human FL Naive CD4 exon-level [PGD_926_HTA]

description:
PGD_926_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Human FL Naive CD4 exon-level [PGD_930_HTA]

description:
PGD_930_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Cell_BJF_Trajectory_B_PDL_3_Replicate_1


title: MB231_TWEAK_K27_rep2


title: MB231_TWEAK_K27_rep1


title: Human tonsil Naive CD4 exon-level [PGD_918_HTA]

description:
PGD_918_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis

source_name: Healthy donor

value: tonsil


title: MB231_TWEAK_K27_rep3


title: Human FL Tfh exon-level [PGD_925_HTA]

description:
PGD_925_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: MB231_UT_K27_rep2


title: MB231_UT_K27_rep3


title: Human FL Naive CD4 exon-level [PGD_914_HTA]

description:
PGD_914_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Cell_BJF_Trajectory_B_PDL_35_Replicate_1


title: MB231_TWEAK_hiChIP_technical_rep2

data_processing:
library strategy: HiChIP
Sequencing reads were aligned to hg38 with BWA-MEM
valid ligation events were recorded and sorted, PCR duplicates were removed and bam files were generated with pairtools and SAMtools
Supplementary files format and content: cool files. Contains matrix

extract_protocol:
DNA Extraction performed by Dovetail
Library construction performed by Dovetail


title: MB231_TWEAK_hiChIP_technical_rep1


title: Human tonsil Treg exon-level [PGD_911_HTA]

description:
PGD_911_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: MB231_UT_hiChIP_technical_rep2


title: Human tonsil Tfh exon-level [PGD_909_HTA]

description:
PGD_909_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Human tonsil Treg exon-level [PGD_919_HTA]

description:
PGD_919_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Cell_BJF_Trajectory_B_PDL_20_Replicate_2


title: MB231_UT_hiChIP_technical_rep1


title: Cell_BJF_Trajectory_B_PDL_15_Replicate_1


title: MCF7_TWEAK_ATAC_rep2

extract_protocol:
DNA was extracted by lysing cells in ATAC resuspension buffer containing NP40, TWEEN-20 and Digitonin. Followed by transposition with digitonin and Tn5 transposase
Transposed DNA was amplified through PCR with Nextera DNA CD Indexes


title: Cell_BJF_Trajectory_B_PDL_3_Replicate_2


title: Human FL Tfh exon-level [PGD_913_HTA]

description:
PGD_913_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: MCF7_UT_ATAC_rep2


title: Human tonsil Tfh exon-level [PGD_917_HTA]

description:
PGD_917_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: MB231_input


title: Human tonsil Memory CD4 exon-level [PGD_908_HTA]

description:
PGD_908_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Human FL Memory CD4 exon-level [PGD_916_HTA]

description:
PGD_916_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Human tonsil Memory CD4 exon-level [PGD_920_HTA]

description:
PGD_920_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Cell_BJF_Trajectory_B_PDL_15_Replicate_2


title: Cell_BJF_Trajectory_B_PDL_10_Replicate_1


title: Hs578T_TWEAK_ATAC_rep2


title: Hs578T_UT_ATAC_rep2


title: Cell_BJF_Trajectory_A_PDL_47_Replicate_2


title: Human tonsil Memory CD4 exon-level [PGD_912_HTA]

description:
PGD_912_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Hs578T_TWEAK_ATAC_rep1


title: Human FL Tfr exon-level [PGD_915_HTA]

description:
PGD_915_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: MB231_TWEAK_ATAC_rep3


title: Cell_BJF_Trajectory_A_PDL_47_Replicate_1


title: Hs578T_UT_ATAC_rep1


title: MB231_TWEAK_ATAC_rep2


title: MCF7_TWEAK_ATAC_rep1


title: Cell_BJF_Trajectory_A_PDL_41_Replicate_1


title: Human tonsil Naive CD4 exon-level [PGD_906_HTA]

description:
PGD_906_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: MB231_TWEAK_ATAC_rep1


title: Cell_BJF_Trajectory_A_PDL_34_Replicate_2


title: MB231_UT_ATAC_rep2


title: Cell_BJF_Trajectory_A_PDL_34_Replicate_1


title: MB231_UT_ATAC_rep3


title: Human tonsil Naive CD4 exon-level [PGD_910_HTA]

description:
PGD_910_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: MB231_UT_ATAC_rep1


title: ATAC_H02D60

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

country: China

institute: Fudan University

data_processing:
[scRNA-seq, BCR and TCR] The raw scRNA-seq and paired single-cell BCR and TCR sequencing data were simultaneously processed with subcommand multi in 10× Genomics software CellRanger (version: 6.1.2). The sequencing data were aligned into human reference genome (GRCh38) and VDJ database (GRCh38), and the expected cell number was set to 10,000.
[scATAC-seq] The raw scATAC-seq sequencing data were initially processed using subcommand count in 10× Genomics software CellRanger-ATAC (version: 2.0.0), and the sequencing data were aligned into human reference genome (GRCh38).
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: "barcodes.tsv" files include scRNA-seq barcode information, "features.tsv" files include scRNA-seq gene features and "matrix.mtx" files include scRNA-seq gene expression. "fragments.tsv" files include scATAC-seq filtered fragments, "singlecell.csv" files include the barcode information of single cells in scATAC-seq data.

extract_protocol:
BD Vacutainer K2 EDTA tube (10ml) were used for blood collection. We obtained peripheral venous blood samples by venipunction from six participants. And then used Ficoll density gradient centrifugation (TBD, China) to separate PBMCs. We pre-added 4 mL Ficoll to each 15 mL centrifuge tube. For each participant, equal volumes of blood were carefully layered onto Ficoll and centrifuged at 800 g and RT for 25 min (3 acceleration and 1 brake). After centrifugation, we collected PBMCs with pipette into a 15-ml tube, and diluted up to 15 ml with pre-warmed PBS (TBD, China). After centrifuging for 10 min, at 250 g and RT, PBMC were resuspended in 2 mL Red Blood Cell Lysis Buffer (Solarbio, China). After incubating the cells on ice for 10 min, 8 mL PBS was added, gently mixed, and centrifuged at 4℃ 300 g for 10 min. We resuspended the centrifuged cells in 10ml of pre-prepared washing buffer (1× PBS with 0.04% BSA). The cleaning step was performed at 250 g and 4℃ for 10 min. The second time the cells were resuspended by the cleaning buffer and counted with the Dual Fluorescence Cell Counter (LunaTM fl). After centrifugation, the cells were resuspended in the cell cryopreservation system recommended by 10× Genomics. With about 2×106 cells per milliliter, one-milliliter aliquots were gradually frozen in a freezing box over the course of 24 h at -80℃ before being kept in a vapor-phase liquid nitrogen tank.
[scRNA-seq, BCR and TCR] We selected samples before vaccination and at days 7, 14, 37, and 60 after vaccination for scRNA-seq. The cells were first thawed according to the 10× Genomics protocol (Demonstrated Protocol, CG00039). The thawed cells were then stained with trypan blue and placed under a light microscope to observe the cell state and background. The cells were counted using the Dual Fluorescence Cell Counter (LunaTM fl), and subsequent procedures were performed after confirming that the survival rate was not less than 90%. The ChromiumTM Single cell 5’ Reagent Kit, Chromium Single Cell Human BCR Amplification Kit, and Chromium Single Cell Human TCR Amplification Kit of the Chromium platform (10× Genomics, California, USA) were used to create the scRNA-seq and paired single-cell BCR and TCR libraries in accordance with the Chromium Single Cell 5’ Reagent Kits User Guide (v2 Chemistry Dual Index). On the Illumina HiSeq X Ten platform, generated scRNA-seq libraries were sequenced. The preprocessing of the PE150 Illumina sequencing reads was done using the 10× Genomics software CellRanger (version: 6.1.2).
[scATAC-seq] We selected samples for scATAC-seq before vaccination and 60 days after vaccination. The cells after thawing were used in nuclei isolation following the Nuclei Isolation for Single Cell ATAC Sequencing protocol from 10× Genomics. The cells were lysed for 1.5 min during the lysis stage. The nuclei suspension obtained by cell lysis were stained with trypan blue and then observed under a light microscope. As for scRNA-seq, the nuclear suspension was counted with the Dual Fluorescence Cell Counter (LunaTM fl). Then Chromium Single Cell ATAC Library and Gel Bead Kit (10× Genomics, 1000110) were used for scATAC-seq. Nuclear suspensions at sufficient concentrations were then used in library preparation using the 10× Genomics Single Cell ATAC Kits following the manufacturer’s protocol.

tag: source

value: Peripheral blood mononuclear cell (PBMC)

tag: library

value: scATAC-seq

tag: donor group

value: HC (Health control)

tag: donor

tag: time point

value: Day 60

value: PBMC


title: ATAC_H01D60


title: Cell_BJF_Trajectory_A_PDL_30_Replicate_2


title: ATAC_H02D0

value: Day 0


title: ATAC_P01D60

value: SLE (systemic lupus erythematosus)


title: ATAC_H01D0


title: Human FL Tfr exon-level [PGD_927_HTA]

description:
PGD_927_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis

tag: tissue


title: Human tonsil Tfh exon-level [PGD_905_HTA]

description:
PGD_905_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: Cell_BJF_Trajectory_A_PDL_30_Replicate_1


title: Cell_BJF_Trajectory_A_PDL_20_Replicate_2


title: ATAC_P01D0


title: ATAC_E02D60


title: RNA_H02D14

value: scRNA-seq

value: Day 7


title: Cell_BJF_Trajectory_A_PDL_20_Replicate_1


title: RNA_H02D60

value: Day 14


title: Cell_BJF_Trajectory_A_PDL_2.3_Replicate_2


title: RNA_H02D0


title: RNA_H01D7


title: Cell_BJF_Trajectory_A_PDL_2.3_Replicate_1


title: Cell_BJF_Trajectory_A_PDL_14_Replicate_1


title: RNA_H01D60


title: Human tonsil Treg exon-level [PGD_907_HTA]

description:
PGD_907_HTA.CEL
RMA expression value derived from Expression Console software ;  exon analysis


title: RNA_H01D14


title: RNA_H01D0


title: Cell_BJF_Trajectory_A_PDL_10_Replicate_1


title: RNA_P01D60


title: RNA_P01D0


title: RNA_E04D14


title: RNA_E04D0


title: ATAC_E02D0


title: Cell_BJF_Trajectory_DeepSen_PDL_104_Replicate_1


title: RNA_E02D60


title: RNA_H02D7


title: Cell_BJF_Trajectory_A_PDL_10


title: RNA_E01D60


title: BMN/PAZA_Low_dose

city: Pittsburgh

first: Zhangyi

last: Luo

state: PA

address: 4041 Bigelow Blvd, Apt 112

institute: University of Pittsburgh

data_processing:
Data was analyzed by following HISAT2-Stringtie-Ballgown workflow published on Nature Protocol.(Pertea, M., Kim, D., Pertea, G. et al, Nat Protoc 11, 1650–1667 (2016).)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

growth_protocol: Cells were maintained in RPMI 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA prepared by University of Pittsburgh Sequencing Core
Library was prepared by University of Pittsburgh Sequencing Core

treatment_protocol: Cells were treated with various treatment accordingly for 72h.

value: Lung

value: Caner cell

value: LLC cells

value: BMN (low dose)+PAZA


title: RNA_E04D60


title: PAZA

description: PA

value: PAZA


title: Control

description: Con

value: Control


title: Cell_BJF_Trajectory_DeepSen_PDL_104_Replicate_2

value: Male

value: Fibroblast


title: BMN

description: B

value: BMN


title: Cell_BJF_Trajectory_B_PDL_38


title: Cell_BJF_Trajectory_B_PDL_26


title: Cell_BJF_Trajectory_B_PDL_10


title: Cell_BJF_Trajectory_A_PDL_26


title: IL-18R-CD103-GFP- cells

city: Brisbane

first: Qiutong

last: Huang

state: QLD

address: 37 Kent Street

country: Australia

institute: The University of Queensland

data_processing:
The demultiplexing, barcode processing and  gene counting  were made using the CellRanger 6.0.1 software.
Assembly: mm10-2020-A
Supplementary files format and content: CellRanger output files: CD103_GFPbarcodes.tsv.gz, CD103_GFPfeatures.tsv.gz, CD103_GFPmatrix.mtx.gz
Supplementary files format and content: CellRanger output files: DNbarcodes.tsv.gz, DNfeatures.tsv.gz, DNmatrix.mtx.gz
Supplementary files format and content: CellRanger output files: ST2barcodes.tsv.gz, ST2features.tsv.gz, ST2matrix.mtx.gz

extract_protocol:
Lungs were transcardically perfused through the right ventricle with PBS to remove blood from the organ. Each lobe of the lung was separated and digested in 1 mg/ml collagenase type III (Worthington), 200 g/ml DNase I (Roche), 0.4 units/ml Dispase (Gibco) in RPMI1640 medium plus 2% FCS with gentleMACSTM Dissociator (Miltenyi Biotec) using the mouse lung digestion protocol setting. The digested lung tissue was then spun down and the mononuclear cells were isolated on a 40%-80% Percoll gradient. Lymphocytes were recovered from the interface and were washed twice with PBS. Live CD45+lin-CD90.2+IL-7R+ were purified using flow cytometry.
Library was prepared using 10X Genomics protocols using the Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index)

value: Lymphocytes


title: RNA_E02D0

value: Peripheral blood mononuclear cell (PBMC)


title: IL-18R+CD103+GFP- and IL-18R+CD103-GFP+ cells


title: Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide-/- C57BL/6J, biol rep1

city: Paris

first: François-Xavier

last: MAUVAIS

address: 160 rue de Vaugirard

data_processing:
Sequence reads were mapped to GRCm38 from Ensembl release 101 using STAR v.2.7.1a with the following parameters : --twopassMode Basic --sjdbOverhang 74 --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat --outSAMunmapped Within --outFilterType BySJout --quantMode TranscriptomeSAM
Read count were performed using RSEM v1.3.1) with the AlignedtoTranscriptome bam files from STAR
Supplementary files format and content: tab-delimited text files including RSEM expected count, FPKM and TPM values for each sample

source_name: Pancreas

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng of high-quality total RNA sample (RIN>6.5) was used for the construction of sequencing libraries.
RNA-seq libraries for RNA-seq were prepared using NEBNext low input RNA library prep kit (NEB) according to manufacturer's instructions.

treatment_protocol: 10-weeks-old female Ide-/- and Ide+/+ C57BL/6J mice were fed with a high-fat diet for 2 weeks (D12492. Rodent Diet With 60 kcal% Fat, Brogaarden, Denmark).

value: Pancreas

value: Hand-picked pancreatic islets

value: Female

value: Ide-/-

value: 2-weeks high-fat diet

tag: age at_treatment_initiation

value: 10 weeks-old


title: Cell_BJF_Trajectory_A_PDL_42

tag: cell type


title: Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide-/- C57BL/6J, biol rep3

tag: genotype


title: Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide-/- C57BL/6J, biol rep2


title: RNA_E01D14

value: scRNA-seq

value: SLE (systemic lupus erythematosus)

value: Day 14

value: PBMC


title: Cell_BJF_Trajectory_A_PDL_38


title: RNA_E01D0

value: Day 0


title: BMN/PAZA_High_dose

value: Lung

value: Caner cell

value: LLC cells

value: BMN (high dose)+PAZA


title: Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide+/+ C57BL/6J, biol rep5

value: Ide+/+


title: Cell_BJF_Trajectory_B_PDL_24

value: Male

value: Fibroblast


title: Cell_BJF_Trajectory_B_PDL_45_Replicate_2


title: Cell_BJF_Trajectory_B_PDL_20_Replicate_1


title: MB231_UT_K27_rep1

value: Breast

value: Breast Cancer

value: Untreated


title: Cell_BJF_Trajectory_A_PDL_4


title: Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide+/+ C57BL/6J, biol rep3

value: Pancreas

value: Hand-picked pancreatic islets

value: Female

value: 2-weeks high-fat diet


title: Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide+/+ C57BL/6J, biol rep1

value: 10 weeks-old


title: Cell_BJF_Trajectory_B_PDL_4


title: Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide+/+ C57BL/6J, biol rep4


title: IL-18R-ST2+

value: Lymphocytes


title: Cell_BJF_Trajectory_B_PDL_22


title: Cell_BJF_Trajectory_A_PDL_40


title: Pancreas, hand-picked pancreatic islets, 2-weeks high-fat diet, Ide+/+ C57BL/6J, biol rep2


title: Cell_BJF_Trajectory_A_PDL_24


title: Cell_BJF_Trajectory_B_PDL_8


title: Cell_BJF_Trajectory_B_PDL_40


title: 80 NOD-Female-5

city: Tuskegee

first: Sunila

last: Mahavadi

state: Alabama

address: 1200 W. Montgomery Rd, Carver Research Building, Room #1

department: Biology

institute: Tuskegee University

data_processing:
MiSeq Control Software, MiSeq Reporter Software, Bismark
Low quality nucleotides and adapter sequences were trimmed off during analysis QC MiSeq Reporter Software
Sequence reads were aligned back to the reference genome using Bismark. Index files were constructed using the bismark_genome_preparation command and the entire reference genome. The non-directional parameter was applied while running Bismark. All other parameters were set to default.
Nucleotides and amplicons were trimmed off during methylation calling. The methylation level of each sampled cytosine was estimated as the number of reporting a C, divided by the total number or reads reporting C or T.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files includes raw counts for each sample

source_name: Colon

extract_protocol:
The DNA was extracted and the samples were bisulfite converted by using EZ DNA Methylation-Lightning ™ Kit according to manufacturer's instructions. The samples were pooled, purified using DNA Clean & Concentration ™ Kit.
Targeted bisulfite Seq; DNA methylation was assessed by EZ DNA Methylation-Lighning ™ Kit (Zymo Research, D5030), according to the manufacturer's instruction.

value: Colon

value: NOD


title: Cell_BJF_Trajectory_A_PDL_22


title: 79 NOD-Female-4


title: Cell_BJF_Trajectory_A_PDL_8


title: 78 NOD-Female-3


title: Cell_BJF_Trajectory_B_PDL_42


title: 77 NOD-Female-2


title: 76 NOD-Female-1


title: Mouse Mammary Fibroblasts from PtenWt female mice 8-9 weeks of age [fib_Wt_rep 2]

city: Charleston

first: Michael

middle: C

last: Ostrowski

state: SC

address: 86 Jonathan Lucas street

department: Biochemistry and Molecular Biology

institute: Medical University of South Carolina

hyb_protocol: Following fragmentation, 15ug of cRNA was hybridized for 16 hours at 45°C on Affymetrix Mouse 430.2 Array GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetric GeneChip Scanner 3000

data_processing: Data were processed using Affymetrix Expression Console software. Robust Multichip Average (RMA) method was used to do background correction, quantile normalization, and expression level summarization.

label: Biotin

organism: Mus

label_protocol: Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1ug total RNA (Expression Analysis Technical Manual, 2005, Affymetrix)

growth_protocol: Mammary glands were dissected from 8-week-old female mice, minced and digested with collagenase (0.15% Collagenase I, 160 U ml-1 hyaluonidase, 1 μg ml-1 hydrocortisone and 10 μg ml-1 insulin with penicillin and streptomycin) in a 5% CO2 incubator overnight at 37 °C. Collagenase was neutralized with 10% FBS–DMEM medium. Digested tissue was resuspended in medium and subjected to gravity for 12–15 min. Pellets were washed three times to collect epithelial organoids, and supernatants were subjected four more times to gravity sedimentation and then cultured.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Fibroblasts were grown in 10% FBS DMEM in a 37° incubator with 5% CO2

value: female

tag: age

value: 8-9 weeks

value: Mouse Mammary Fibroblasts


title: 74 NOD-Female-4

source_name: Stomach

value: Stomach


title: 75 NOD-Female-5


title: Cell_BJF_hTERT_Trajectory_A_PDL_18

value: Male


title: Mouse Mammary Fibroblasts from PtenWt female mice 8-9 weeks of age [fib_Wt_rep 3]


title: Mouse Mammary Fibroblasts from Pten341V/f mice [fib_Pten341_rep 1]

source_name: Mouse Mammary Fibroblasts from Pten341V/f female mice 8-9 weeks of age

value: PtenF341V/f ; Fsp-cre


title: Mouse Mammary Fibroblasts from PtenWt female mice 8-9 weeks of age [fib_Wt_rep 4]


title: Cell_BJF_hTERT_Trajectory_B_PDL_8

value: Fibroblast


title: Mouse Mammary Fibroblasts from Pten341V/f female mice 8-9 weeks of age [fib_Pten341_rep 3]


title: Mouse Mammary Fibroblasts from Ptennull female mice 8-9 weeks of age [fib_PtenNull_rep 3]

value: Ptenf/f; Fsp-cre


title: Cell_BJF_hTERT_Trajectory_A_PDL_8


title: Mouse Mammary Fibroblasts from Ptennull female mice 8-9 weeks of age [fib_PtenNull_rep 2]


title: Mouse Mammary Fibroblasts from Ptennull female mice 8-9 weeks of age [fib_PtenNull_rep 1]


title: 71 NOD-Female-1


title: Mouse Mammary Fibroblasts from Ptennull female mice 8-9 weeks of age [fib_PtenNull_rep 4]


title: Mouse Mammary Fibroblasts from Pten341V/f female mice 8-9 weeks of age [fib_Pten341_rep 2]


title: 70 Control-Female-5

value: Control


title: 68 Control-Female-3


title: Cell_BJF_hTERT_Trajectory_A_PDL_2


title: 73 NOD-Female-3


title: Mouse Mammary Fibroblasts from PtenWt female mice 8-9 weeks of age [fib_Wt_rep 1]


title: 72 NOD-Female-2


title: Cell_BJF_hTERT_Trajectory_B_PDL_2


title: 67 Control-Female-2


title: 66 Control-Female-1


title: 65 Control-Female-5


title: 64 Control-Female-4


title: Cell_BJF_hTERT_Trajectory_A_PDL_24_Replicate_2


title: 63 Control-Female-3


title: 62 Control-Female-2


title: Cell_BJF_hTERT_Trajectory_A_PDL_6


title: 61 Control-Female-1


title: 58 NOD-Male-3


title: 69 Control-Female-4


title: Cell_BJF_hTERT_Trajectory_B_PDL_18


title: 57 NOD-Male-2


title: 55 NOD-Male-5


title: 56 NOD-Male-1


title: Cell_BJF_hTERT_Trajectory_B_PDL_6


title: Cell_BJF_hTERT_Trajectory_A_PDL_36


title: 54 NOD-Male-4


title: 51 NOD-Male-1


title: 50 Control-Male-5


title: 52 NOD-Male-2


title: 49 Control-Male-4


title: Cell_BJF_hTERT_Trajectory_A_PDL_26


title: MCF7_UT_ATAC_rep1

value: Breast

value: Breast Cancer

value: Untreated


title: 53 NOD-Male-3


title: Cell_BJF_hTERT_Trajectory_B_PDL_36


title: Cell_BJF_hTERT_Trajectory_A_PDL_34


title: 48 Control-Male-3


title: Cell_BJF_hTERT_Trajectory_B_PDL_24


title: 47 Control-Male-2


title: Cell_BJF_hTERT_Trajectory_A_PDL_4


title: 44 Control-Male-4

source_name: stomach

value: stomach


title: 60 NOD-Male-5


title: Cell_BJF_hTERT_Trajectory_B_PDL_24_Replicate_2


title: 45 Control-Male-5


title: 46 Control-Male-1


title: 59 NOD-Male-4


title: 43 Control-Male-3


title: Cell_BJF_hTERT_Trajectory_A_PDL_24


title: 41 Control-Male-1


title: Cell_BJF_hTERT_Trajectory_A_PDL_28


title: Microbiota of stool from mice AD45

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

description: 16s rRNA v3-v4 sequencing of mice stool

data_processing:
demultiplexing from raw to demultiplexed fastq files please contact IGA Technology Services (Udine, Italy)
primer check and trimming qiime cutadapt trim-paired --i-demultiplexed-sequences demux-paired-end.qza --p-front-f CCTACGGGNGGCWGCAG --p-front-r GACTACNVGGGTWTCTAATCC --p-cores 7 --o-trimmed-sequences trimmed-seqs.qza --p-discard-untrimmed –verbose
quality check qiime demux summarize --i-data trimmed-seqs.qza --o-visualization demux.qzv --p-n 500000
ASV generation qiime dada2 denoise-paired --i-demultiplexed-seqs trimmed-seqs.qza --p-trim-left-f 5 --p-trim-left-r 0 --p-trunc-len-f 274 --p-trunc-len-r 174 --o-table table.qza --o-representative-sequences rep-seqs.qza --o-denoising-stats denoising-stats.qza --p-n-threads 6
taxonomic assignment qiime feature-classifier classify-sklearn --i-classifier SILVA_138_V3V4_BayesClassifier.qza --i-reads rep-seqs.qza --o-classification taxonomy.qza
further analyses R software (see the relative script publicly available at github.com/LeandroD94)
Assembly: NA
Supplementary files format and content: dna-sequences.fasta: text containing every processed ASV code and sequence
Supplementary files format and content: Feature_table.tsv: TSV text file containing the abundance table
Supplementary files format and content: taxonomy.tsv: TSV text file containing the complete taxonomic classification of the reference sequence
Library strategy: 16s rRNA-seq

source_name: Stool

extract_protocol:
Genomic DNA was extracted using the DNeasy PowerSoil Pro Kit (Qiagen, Hilden, Germany)
Illumina 16S Metagenomic Sequencing Library Preparation protocol ( see https://emea.support.illumina.com)

value: Stool


title: Microbiota of stool from mice AD44

description: 16s rRNA v3-v4 sequencing of mice stool


title: Cell_BJF_hTERT_Trajectory_B_PDL_4


title: Cell_BJF_hTERT_Trajectory_A_PDL_22


title: Microbiota of stool from mice AD43

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD40

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD42

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD41

description: 16s rRNA v3-v4 sequencing of mice stool


title: Cell_BJF_hTERT_Trajectory_B_PDL_34


title: Microbiota of stool from mice AD38

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD37

description: 16s rRNA v3-v4 sequencing of mice stool

value: WT


title: Microbiota of stool from mice AD34

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD35

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD39

description: 16s rRNA v3-v4 sequencing of mice stool


title: WES Runx1 Mir-146 KO 3

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

description: Runx1 Mir-146 KO 3

data_processing:
The quality of reads were checked using FastQC (v0.11.2).
Paired-end reads were aligned against the GRCm38 genome using BWA (v0.7.17).
Germline SNP and INDEL variants were separately detected using VarScan (v2.3.9) and Samtools (v1.8.0).
The exon target capture info was from Agilent SureSelect XT Mouse All Exon V1
Variants were annotated using VEP (v96).
Assembly: GRCm38
Supplementary files format and content: Predicted SNP and INDEL reports in the VCF format

source_name: BM

growth_protocol: genomic DNA isolated from FACS sorted BM GFP+/lin-/ckit+/Sca+ cells from WT/vector (n=3), WT/RUNX1mut (n=3), miR-146aKO/vector (n = 3), and miR-146aKO/RUNX1mut secondary transplanted mice were submitted to Otogenetics Corporation (Atlanta, GA, USA) for mouse exome capture and sequencing

extract_protocol:
gDNA was extracted using the AllPrep micro kit from Qiagen following manufacturer recommendations
SureSelect_Mouse_All_Exon_V1_Annotated_mm10_liftover_09212015.bed
Mouse exome sequencing from gDNA; Initial sample QC; Illumina library prep/QC; Agilent SureSelect mouse(51Mb), capture/QC; HiSeq2000/2500 PE100-125, designate average coverage of 30x
Exome sequencing

value: BM

value: primary cell

value: Hematopoietic stem and progenitor cells


title: Microbiota of stool from mice AD32

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD36

description: 16s rRNA v3-v4 sequencing of mice stool


title: WES Runx1 Mir-146 KO 2

description: Runx1 Mir-146 KO 2


title: WES Mir-146 KO/Empty 3

description: Mir-146 KO/Empty 3


title: Microbiota of stool from mice AD33

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD30

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD29

description: 16s rRNA v3-v4 sequencing of mice stool

value: DSS


title: Microbiota of stool from mice AD28

description: 16s rRNA v3-v4 sequencing of mice stool


title: WES Empty 3

description: Empty 3

source_name: spleen

value: spleen

value: miR-146a wildtype/Runx1 wildtype


title: WES Runx1 Mir-146 KO 1

description: Runx1 Mir-146 KO 1

source_name: Spleen

value: Spleen


title: Microbiota of stool from mice AD27

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD26

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD25

description: 16s rRNA v3-v4 sequencing of mice stool


title: Cell_BJF_hTERT_Trajectory_B_PDL_38

value: Male


title: Microbiota of stool from mice AD24

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD23

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD22

description: 16s rRNA v3-v4 sequencing of mice stool


title: WES Empty 1

description: Empty 1


title: WES Runx1 3

description: Runx1 3


title: Microbiota of stool from mice AD21

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD20

description: 16s rRNA v3-v4 sequencing of mice stool


title: WES Runx1 2

description: Runx1 2


title: WES Runx1 1

description: Runx1 1


title: Microbiota of stool from mice AD31

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD17

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD16

description: 16s rRNA v3-v4 sequencing of mice stool


title: WES Mir-146 KO/Empty 2

description: Mir-146 KO/Empty 2


title: Microbiota of stool from mice AD15

description: 16s rRNA v3-v4 sequencing of mice stool


title: WES Mir-146 KO/Empty 1

description: Mir-146 KO/Empty 1


title: Microbiota of stool from mice AD14

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD12

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD13

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD11

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD10

description: 16s rRNA v3-v4 sequencing of mice stool


title: WES Empty 2

description: Empty 2


title: sh-DNMT1 Cal27-2

city: Chengdu

first: Yangfan

last: Liu

state: Sichuan

address: People South Street

institute: Sichuan University

description: sh-DNMT1 Cal27 cells

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium 850k Human Methylation Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing:
Empower (R) software minfi package
Matrix processed.txt = Average Beta
Matrix_signal_intensities.txt = Unmethylated and methylated signal intensities

label: Cy5 and Cy3

label_protocol: Standard lllumina Protocol

growth_protocol: cells in exponential growth phase were collected from T25 culture flasks for experiments

extract_protocol: genomic DNA was extracted and purifed from LBC samples using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: sh-DNMT1 Cal27 cells were treated by short hairpin RNA directed against DNMT1, sh-NC Cal27 cells were treated by short hairpin RNA negative control

tag: disease state

value: OSCC


title: Microbiota of stool from mice AD8

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD9

description: 16s rRNA v3-v4 sequencing of mice stool


title: sh-NC Cal27-2

description: sh-NC Cal27 cells

value: short hairpin RNA negative control


title: Microbiota of stool from mice AD5

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD19

description: 16s rRNA v3-v4 sequencing of mice stool


title: Microbiota of stool from mice AD18

description: 16s rRNA v3-v4 sequencing of mice stool


title: sh-NC Cal27-3

description: sh-NC Cal27 cells


title: Microbiota of stool from mice AD3

description: 16s rRNA v3-v4 sequencing of mice stool


title: Cal27-3

description: untreated Cal27 cells

value: without treatment


title: Microbiota of stool from mice AD7

description: 16s rRNA v3-v4 sequencing of mice stool


title: Cal27-2

description: untreated Cal27 cells


title: soy peptide-diet fed social isolation mouse #2 [SP2]

city: Shinagawa-ku

first: Hideki

last: Tamura

state: Tokyo

country: Japan

institute: Hoshi University

data_processing:
library strategy: 16S rRNA-seq
Flora Genesis software
Microbial species were identified based on 16S rRNA gene sequence data using Flora Genesis software.
Assembly: BLAST 2.2.22 / gg_otus-13_8-release
Supplementary files format and content: Excel file includes microbial species-specific read number for each Sample

source_name: Fecal

extract_protocol:
Mouse fecal samples were collected directly into tubes from which microbial DNA were extracted.
The V3-V4 regions of 16S rRNA genes were amplified using PCR with individually barcoded universal primers and sequenced by MiSeq next-generation sequencer with an average depth of 75,000 reads per sample.

treatment_protocol: Group-house and social isolation mice were fed either a control diet, containing 14% casein, or a soy peptide diet, containing 7% casein plus 7% soy peptides for 4 weeks post-weaning.

value: Fecal

value: gut microbial

value: soy peptide diet / social isolation


title: soy peptide-diet fed social isolation mouse #3 [SP3]


title: control diet-fed social isolation mouse #3 [SC3]

value: control diet / social isolation


title: soy peptide-diet fed social isolation mouse #1 [SP1]


title: NOK-2

description: normal oral keratinocytes cells

value: NOK

value: normal


title: control diet-fed social isolation mouse #2 [SC2]

value: WT


title: sh-DNMT1 Cal27-1

description: sh-DNMT1 Cal27 cells

value: short hairpin RNA directed against DNMT1


title: NOK-1

description: normal oral keratinocytes cells


title: soy peptide-diet fed group-house mouse #3 [GP3]

value: soy peptide diet / group-house


title: control diet-fed social isolation mouse #1 [SC1]


title: soy peptide-diet fed group-house mouse #2 [GP2]


title: sh-DNMT1 Cal27-4

description: sh-DNMT1 Cal27 cells


title: Microbiota of stool from mice AD4

description: 16s rRNA v3-v4 sequencing of mice stool

value: Stool

value: DSS


title: sh-DNMT1 Cal27-3

description: sh-DNMT1 Cal27 cells


title: control diet-fed group-house mouse #3 [GC3]

value: control diet / group-house


title: soy peptide-diet fed group-house mouse #1 [GP1]


title: sh-NC Cal27-1

description: sh-NC Cal27 cells


title: Microbiota of stool from mice AD2

description: 16s rRNA v3-v4 sequencing of mice stool


title: control diet-fed group-house mouse #1 [GC1]


title: Microbiota of stool from mice AD1

description: 16s rRNA v3-v4 sequencing of mice stool


title: Cal27-1

description: untreated Cal27 cells


title: NOK-3

description: normal oral keratinocytes cells


title: GL261-MUT Mouse 5

city: Boston

first: Eric

last: Grewal

state: MA

address: 55 Fruit Street

institute: Massachusetts General Hospital

data_processing: After RNA sequencing, each raw sample file (.RCC format) was uploaded to the automated RNA-sequencing data processing and analysis software, Rosalind (Rosalind Bio). These files underwent automatic read mapping, normalization, and quality control.

source_name: IDH-mutant murine GL261 tumor

extract_protocol: Freshly dissected murine tumors were mechanically dissociated and digested into tumor lysates prior to purification for total RNA using the Qiagen Rneasy kit (74104).

value: IDH-mutant murine GL261 tumor

tag: idh status

value: Mutant


title: patient_5

city: Zhengzhou

first: huijuan

last: Tian

state: Henan

address: No.1 Jianshe East Road, Zhengzhou, (China)

institute: The First Affiliated Hospital of Zhengzhou University

description: xujunling

data_processing:
Illumina bcl2fastq software used for basecalling.
The raw reads were trimmed of low-quality bases using a FASTX-Toolkit (v.0.0.13;http://hannonlab.cshl.edu/fastx_toolkit/).
Clean reads were aligned to the human GRCh38 genome by HISAT2
Uniquely mapped reads were ultimately used to calculate read number and reads per kilobase of exon per million fragments mapped (FPKM) for each gene
In order to predict credible lncRNA, we used four software to predict lncRNA: CPC2[3], LGC[4], CNCI[5] and CPAT[6].We counted the noncoding transcripts identified by the above four analysis software
Assembly: hg38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: renal tissue

extract_protocol:
Total RNA was extracted using TRIzol reagent and was further purified with two phenol-chloroform treatments. To remove DNA, the purified RNA was then treated with RNase-free RQ1 DNase (Promega Corp.) and its quality and quantity were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using a Smartspec Plus (Bio-Rad Laboratories, Inc.). The integrity of RNA was then verified by 1.5% agarose gel electrophoresis.
A total of 10 μg total RNA from each sample was used to prepare a directional RNA-seq library. First, the polyadenylated mRNAs were concentrated with oligo (dT)-conjugated magnetic beads (Invitrogen; Thermo Fisher Scientific, Inc.). The concentrated mRNAs were then iron-fragmented at 95˚C, end-repaired and ligated to a 5′ adaptor. RT was performed with RT primer harboring a 3′ adaptor sequence and randomized hexamer. The purified cDNAs were amplified and stored at -80˚C until they were used for sequencing. Following the manufacturer’s instructions, the libraries were prepared for high-throughput sequencing. The Illumina Novaseq 2000 (Illumina, Inc.) was used to collect data from 150-bp pair-end sequencing (Illumina, Inc).

value: renal tissue

tag: disease

value: primary glomerulonephritis


title: control diet-fed group-house mouse #2 [GC2]

tag: treatment


title: patient_4

description: xiesuxia


title: patient_2

description: guohaunyin


title: GL261-MUT Mouse 3


title: patient_1

description: guozhenghua


title: patient_3

description: qinyingying


title: GL261-MUT Mouse 2


title: health_2

value: healthy


title: health_4

description: ZC


title: health_3


title: health_1


title: GL261-MUT Mouse 1


title: GL261-WT Mouse 5

source_name: IDH-wildtype murine GL261 tumor

value: IDH-wildtype murine GL261 tumor

value: Wildtype


title: GL261-WT Mouse 4


title: GL261-WT Mouse 3


title: kidney in db/db+Irbsartan mice, biological rep1 [db/db-40]

city: Beijing

first: Haojun

last: Zhang

state: Beijing

address: 2 YingHua Dongjie, Chaoyang District

department: Institute of Clinical Medical Sciences

institute: China-Japan Friendship Hospital

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_40_(MoGene-2_0-st).db.rma-gene-full-Signal

hyb_protocol: 15µg fragmented cRNA, with contol oligo B2 and eukaryotic hybridization controls (bioB, bioC, bioD, cre) was hybridized to the Affymetrix Mouse Genome 430 2.0 array at 45℃ for 16 hours. After hybridization, the GeneChip arrays were washed, and then stained with streptavidin phycoerythrinonan (SAPE) with Affymetrix Fluidics Station 450

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.

data_processing: Microarray data were analyzed using Affymetrix Expression Console and Transcriptome Analysis Software(TAC) 3.0 and normalized using the Robust Multiarray Average (RMA) method.

source_name: kidney in db/db+Irbsartan mice

label_protocol: 100ng of total RNA was used for cDNA synthesis, and produce biotin-tagged cRNA with GeneChip IVT Labeling kit (Affymetrix).

tag: strain

value: Diabetic db/db

value: male

value: irbsartan for 12 weeks

value: kidney


title: kidney in db/db mice, biological rep3 [db/db-16]

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_16_(MoGene-2_0-st).db.rma-gene-full-Signal

source_name: kidney in db/db mice

value: vehcle for 12 weeks


title: kidney in db/m mice, biological rep3 [db/m-8]

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_8_(MoGene-2_0-st).db.rma-gene-full-Signal

source_name: kidney in db/m mice

value: db/m


title: kidney in db/m mice, biological rep2 [db/m-3]

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_3_(MoGene-2_0-st).db.rma-gene-full-Signal


title: kidney in db/db+Irbsartan mice, biological rep3 [db/db-42]

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_42_(MoGene-2_0-st).db.rma-gene-full-Signal


title: kidney in db/db+Irbsartan mice, biological rep2 [db/db-41]

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_41_(MoGene-2_0-st).db.rma-gene-full-Signal


title: kidney in db/db mice, biological rep2 [db/db-14]

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_14_(MoGene-2_0-st).db.rma-gene-full-Signal


title: kidney in db/db mice, biological rep1 [db/db-10]

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_10_(MoGene-2_0-st).db.rma-gene-full-Signal


title: kidney in db/m mice, biological rep1 [db/m-1]

description:
Effects of Irbesartan on Gene Expression Profiles in Kidney Tissues of Diabetic db/db Mice
131119-131171B_1_(MoGene-2_0-st).db.rma-gene-full-Signal


title: ES2-EC359- 1

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

data_processing:
Illumina Casava v1.8.2 software used for base-calling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using TopHat v2.0.8b
gene count measurements were obtained using HTSeq-count
Assembly: hg19
Supplementary files format and content: The processed data files are in tabular format.  The first column contains the gene symbols and the second column contain the read counts of the gene using htseq-count

source_name: ES2 cells treated with LIFR inhibitor EC359

growth_protocol: ES2 cells were cultured in RPMI media supplemented with 10% FBS

extract_protocol:
ES2 cells are treated with vehicle (0.1% DMSO) or EC359 (10 nM) for 12 hours and total RNA was isolated using RNeasy mini kit using manufacturer’s protocol (Qiagen, Valencia, CA).
Total RNA samples about 500ng were used for sequencing library preparation according to Illumina TruSeq Stradned mRNA Sample Preparation Guide (Illumina Cat. #: RS-122-2201). Each library was bar-coded and then pooled for cluster generation and sequencing run with 50bp single-end (SE) sequencing protocol.

treatment_protocol: Total RNA was isolated from ES2 cells that are treated with vehicle or EC359 and subjected to RNAseq analysis

tag: cell line

value: Ovarian cancer cell line


title: ES2-Vehicle- 2

source_name: ES2 cells treated with vehicle

value: vehicle (0.1% DMSO) for 12 h


title: GL261-WT Mouse 2


title: Sm_NecLo_Sta_Rep3

city: Baltimore

first: Jeffrey

last: Gardner

state: MD

address: 1000 Hilltop Circle

institute: University of Maryland - Baltimore County

description:
Sm_NecLo_TPM.csv
Necromass_DEG.xlsx

data_processing:
The raw FASTQ files were quality checked, aligned to existing genomes, and analyzed for differential expression using the Galaxy platform. Unless otherwise noted below, default parameters were in all analysis tools used except in cases where strandedness was specified (all RNAseq data were unstranded). Briefly, RNAseq data were concatenated using the concatenate data sets: tail-to-head (cat) tool. Transcript quality was tested using FastQC, which indicated read trimming was unnecessary for any of the files. Transcripts were next aligned to their respective reference genomes using the HISAT2 tool and quantified using the htseq-count tool. Reference genome files for C. japonicus Ueda107 (ASM1922v1) and C. pinensis DSM2588 (ASM2400v1) were obtained from ENSEMBLE, while that for S. marcescens PIC3611 was retrieved from NCBI Refseq (ASM2260299v1). Due to the differences in reference genome sources, the S. marcescens files required a parameter change in the htseq-count ‘feature type’ from ‘gene’ to ‘exon’. Differential gene expression using DESeq2 compared necromass exponential growth to necromass stationary phase for all three species and glucose for Cp and Sm.
Assembly: C. japonicus Ueda107 (ASM1922v1); C. pinensis DSM2588 (ASM2400v1); S. marcescens PIC3611 (ASM2260299v1)
Supplementary files format and content: TPM for biolgical repliates for a given substrate and bacterial species; DEG with p-values for pair-wise comparisons

organism: Serratia marcescens

source_name: Bacterial cell

extract_protocol:
As per the protocol described in PMID: 22949721
Ribosomal RNA Depletion; RNA Fragmentation and Random Priming; Fist and Second Strand cDNA synthesis; End Repair with 5' phosphorylation and dA-Tailing; Adapter ligation with PCR enrichment; Sequencing

value: Bacterial cell

value: WT

tag: group

value: NecLo

tag: growth phase

value: Sta


title: ES2-Vehicle- 1


title: GL261-WT Mouse 1


title: Sm_NecLo_Sta_Rep1

description:
Sm_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Sm_NecLo_Sta_Rep2

description:
Sm_NecLo_TPM.csv
Necromass_DEG.xlsx


title: GL261-MUT Mouse 4

value: IDH-mutant murine GL261 tumor

value: Mutant


title: Sm_NecLo_Log_Rep3

description:
Sm_NecLo_TPM.csv
Necromass_DEG.xlsx

value: Log


title: Sm_NecLo_Log_Rep1

description:
Sm_NecLo_TPM.csv
Necromass_DEG.xlsx


title: 42 Control-Male-2

value: stomach

value: Control


title: Sm_NecLo_Log_Rep2

description:
Sm_NecLo_TPM.csv
Necromass_DEG.xlsx


title: Human FL Tfr gene-level [PGD_931_HTA]

description:
PGD_931_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis

data_processing: CEL files were further processed with Affymetrix Expression Console software version 1.3.1 using Robust Multi-array Average (RMA) algorithms with default settings at the gene and exon levels.

source_name: Follicular Lymphoma donor

extract_protocol:
Lymphoid cells were recovered by perfusion of FL lymph node (LN) biopsies or non-malignant tonsils, enriched using Ficoll gradient
First, CD19+/CD14+/CD8+/CD16+ cell populations were targeted by their dedicated mouse anti-human monoclonal antibody, Second : an incubation with goat anti-mouse magnetic beads allowed CD4+ T enrichement. Third, subsets of interest were sorted according to their known phenotype using a FACSAria flow cytometer
RNA was isolated from 0,5 to 10M sorted cells with the RNeasy AllPrep Micro Kit (Qiagen), according to the manufacturer’s instructions.

value: Lymph node


title: Human FL Tfh gene-level [PGD_929_HTA]

description:
PGD_929_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human FL Naive CD4 gene-level [PGD_930_HTA]

description:
PGD_930_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human FL Memory CD4 gene-level [PGD_928_HTA]

description:
PGD_928_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Sm_NecHi_Sta_Rep3

description:
Sm_NecHi_TPM.csv
Necromass_DEG.xlsx

value: NecHi


title: Human tonsil Memory CD4 gene-level [PGD_920_HTA]

description:
PGD_920_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis

source_name: Healthy donor

value: tonsil


title: Human FL Memory CD4 gene-level [PGD_932_HTA]

description:
PGD_932_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human FL Tfr gene-level [PGD_927_HTA]

description:
PGD_927_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human tonsil Naive CD4 gene-level [PGD_918_HTA]

description:
PGD_918_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human FL Memory CD4 gene-level [PGD_916_HTA]

description:
PGD_916_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human tonsil Treg gene-level [PGD_919_HTA]

description:
PGD_919_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human FL Naive CD4 gene-level [PGD_926_HTA]

description:
PGD_926_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Sm_NecHi_Sta_Rep2

description:
Sm_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Human tonsil Tfh gene-level [PGD_917_HTA]

description:
PGD_917_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Human FL Tfr gene-level [PGD_915_HTA]

description:
PGD_915_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis


title: Sm_NecHi_Sta_Rep1

description:
Sm_NecHi_TPM.csv
Necromass_DEG.xlsx


title: Human FL Naive CD4 gene-level [PGD_914_HTA]

description:
PGD_914_HTA.CEL
RMA expression value derived from Expression Console software ; genes analysis